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Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024; 22:650-665. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
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Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
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Davin-Regli A, Pagès JM, Vergalli J. The contribution of porins to enterobacterial drug resistance. J Antimicrob Chemother 2024; 79:2460-2470. [PMID: 39205648 DOI: 10.1093/jac/dkae265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
In Enterobacteriaceae, susceptibility to cephalosporins and carbapenems is often associated with membrane and enzymatic barrier resistance. For about 20 years, a large number of Klebsiella pneumoniae, Escherichia coli and Enterobacter cloacae presenting ß-lactam resistance have been isolated from medical clinics. In addition, some of the resistant isolates exhibited alterations in the outer membrane porin OmpC-OmpF orthologues, resulting in the complete absence of gene expression, replacement by another porin or mutations affecting channel properties. Interestingly, for mutations reported in OmpC-OmpF orthologues, major changes in pore function were found to be present in the gene encoding for OmpC. The alterations were located in the constriction region of the porin and the resulting amino acid substitutions were found to induce severe restriction of the lumen diameter and/or alteration of the electrostatic field that governs the diffusion of charged molecules. This functional adaptation through porins maintains the entry of solutes necessary for bacterial growth but critically controls the influx of harmful molecules such as β-lactams at a reduced cost. The data recently published show the importance of understanding the underlying parameters affecting the uptake of antibiotics by infectious bacteria. Furthermore, the development of reliable methods to measure the concentration of antibiotics within bacterial cells is key to combat impermeability-resistance mechanisms.
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Wang HY, Tseng YJ, Lin WY, Wang YC, Lin TW, Hsu JF, Wu MYC, Wu CH, Kalpana S, Lu JJ. Comparison of Multiple Carbapenemase Tests Based on an Unbiased Colony-Selection Method. Biomedicines 2024; 12:2134. [PMID: 39335647 PMCID: PMC11429148 DOI: 10.3390/biomedicines12092134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 08/22/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Carbapenemase-producing organisms (CPOs) present a major threat to public health, demanding precise diagnostic techniques for their detection. Discrepancies among the CPO tests have raised concerns, partly due to limitations in detecting bacterial diversity within host specimens. We explored the impact of an unbiased colony selection on carbapenemase testing and assessed its relevance to various tests. Using the FirstAll method for unbiased colony selection to reduce bias, we compared the results from different methods, namely the modified carbapenem inactivation method/EDTA-modified carbapenem inactivation method (mCIM/eCIM), the Carba5, the CPO panel, and the multiplex PCR (MPCR). We compared the FirstAll method to the conventional colony selection for MPCR with seven CPO species. In addition, we evaluated the test performance on seven CPO species using MPCR as a reference and the FirstAll method as the colony-selection method. The results revealed that the selections from the FirstAll method have improved rates of carbapenemase detection, in comparison to approximately 11.2% of the CPO isolates that were noted to be false negatives in the conventional colony-selection methods. Both the Carba5 test and the CPO panel showed suboptimal performance (sensitivity/specificity: Carba5 74.6%/89.5%, CPO panel 77.2%/74.4%) in comparison to the FirstAll method. The Carba5 test provided specific carbapenemase class assignments, but the CPO panel failed in 18.7% of the cases. The Carba5 test and the CPO panel results correlated well with ceftazidime-avibactam minimal inhibitory concentrations (MICs). The concordance for Class A/D with MICs was 94.7% for Carba5 and 92.7% for the CPO panel; whereas for Class B, it was 86.5% for Carba5 and 75.9% for the CPO panel. In conclusion, FirstAll, as the unbiased colony-selection method, was shown to impact carbapenemase testing. With FirstAll, the diagnostic performance of both the Carba5 and the CPO panel was found to be lower. Furthermore, the utilization of ceftazidime-avibactam guided by either the CPO panel or Carba5 was appropriate.
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Affiliation(s)
- Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu 300044, Taiwan
- 20/20 GeneSystems, Gaithersburg, MD 20877, USA
| | - Yi-Ju Tseng
- Department of Computer Science, National Yang Ming Chiao Tung University, Hsinchu 112304, Taiwan
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Wan-Ying Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Yu-Chiang Wang
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ting-Wei Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Jen-Fu Hsu
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Marie Yung-Chen Wu
- Department of Medicine, MetroWest Medical Center, Framingham, MA 01702, USA
| | - Chiu-Hsiang Wu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
- Department of Laboratory Medicine, Keelung Chang Gung Memorial Hospital, Keelung 204201, Taiwan
| | - Sriram Kalpana
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Jang-Jih Lu
- Division of Clinical Pathology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 23142, Taiwan
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Khoshbayan A, Narimisa N, Elahi Z, Bostanghadiri N, Razavi S, Shariati A. Global prevalence of mutation in the mgrB gene among clinical isolates of colistin-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. Front Microbiol 2024; 15:1386478. [PMID: 38912352 PMCID: PMC11190090 DOI: 10.3389/fmicb.2024.1386478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colistin is used as a last resort for managing infections caused by multidrug-resistant bacteria. However, the high emergence of colistin-resistant strains has restricted the clinical use of this antibiotic in the clinical setting. In the present study, we evaluated the global prevalence of the mutation in the mgrB gene, one of the most important mechanisms of colistin resistance in Klebsiella pneumoniae. Methods Several databases, including Scopus, Medline (via PubMed), and Web of Science, were searched (until August 2023) to identify those studies that address the mgrB mutation in clinical isolates of K. pneumoniae. Using Stata software, the pooled prevalence of mgrB mutation and subgroup analyses for the year of publication, country, continent, mgrB mutation types, and detection methods of mgrB mutation were analyzed. Results Out of the 115 studies included in the analysis, the prevalence of mgrB mutations in colistin-resistant K. pneumoniae isolates was estimated at 65% of isolates, and mgrB variations with insertional inactivation had the highest prevalence among the five investigated mutations with 69%. The year subgroup analysis indicated an increase in mutated mgrB from 46% in 2014 to 61% in 2022. Europe had the highest prevalence of mutated mgrB at 73%, while Africa had the lowest at 54%. Conclusion Mutations in the mgrB gene are reported as one of the most common mechanisms of colistin resistance in K. pneumoniae, and the results of the present study showed that 65% of the reported colistin-resistant K. pneumoniae had a mutation in this gene.
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Affiliation(s)
- Amin Khoshbayan
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Negar Narimisa
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Vice Chancellery of Education and Research, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Narjess Bostanghadiri
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- Molecular and Medicine research center, Khomein University of Medical Sciences, Khomein, Iran
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
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Aihara M, Gotoh Y, Shirahama S, Matsushima Y, Uchiumi T, Kang D, Hayashi T. Generation and maintenance of the circularized multimeric IS26-associated translocatable unit encoding multidrug resistance. Commun Biol 2024; 7:597. [PMID: 38762617 PMCID: PMC11102541 DOI: 10.1038/s42003-024-06312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
In gram-negative bacteria, IS26 often exists in multidrug resistance (MDR) regions, forming a pseudocompound transposon (PCTn) that can be tandemly amplified. It also generates a circular intermediate called the "translocatable unit (TU)", but the TU has been detected only by PCR. Here, we demonstrate that in a Klebsiella pneumoniae MDR clone, mono- and multimeric forms of the TU were generated from the PCTn in a preexisting MDR plasmid where the inserted form of the TU was also tandemly amplified. The two modes of amplification were reproduced by culturing the original clone under antimicrobial selection pressure, and the amplified state was maintained in the absence of antibiotics. Mono- and multimeric forms of the circularized TU were generated in a RecA-dependent manner from the tandemly amplified TU, which can be generated in RecA-dependent and independent manners. These findings provide novel insights into the dynamic processes of genome amplification in bacteria.
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Affiliation(s)
- Masamune Aihara
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan.
- Department of Health Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Saki Shirahama
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Yuichi Matsushima
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Uchiumi
- Department of Health Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Kashiigaoka Rehabilitation Hospital, Fukuoka, Japan
- Department of Medical Laboratory Science, Faculty of Health Sciences, Junshin Gakuen University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Fordham SME, Drobniewski F, Barrow M, Hutchings M, Crowther K, Richards D, Bolton P, Mantzouratou A, Sheridan E. Genetic Analyses of Rare ESBL ST628 Klebsiella pneumoniae Detected during a Protracted Nosocomial Outbreak in the United Kingdom. Microorganisms 2024; 12:883. [PMID: 38792715 PMCID: PMC11124425 DOI: 10.3390/microorganisms12050883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) cultures from a hospital-wide outbreak in the UK, which lasted for over 12 months, were sequenced. We sought to sequence and genetically characterise the outbreak strain. Antibiotic Susceptibility Testing (AST) was performed on 65 K. pneumoniae isolates saved from the outbreak. All isolates were sequenced using the Oxford Nanopore Technologies (ONT) MinION flowcell: 10 isolates, including the isolate with the earliest collection date in 2017, were additionally sequenced on the NovaSeq 6000 platform to build high-accuracy nanopore-illumina assemblies. Among the sequenced strains, 60 were typed as ST628. 96.6% (n = 58/60) ST628 strains harboured a large ~247-kb FIB(K) plasmid carrying up to 11 antimicrobial resistance genes, including the extended-spectrum beta-lactamase (ESBL) gene, blaCTX-M-15. Clonality between the outbreak isolates was confirmed using single nucleotide polymorphism (SNP) typing. The outbreak strains were phylogenetically related to clinical ST628 strains identified in 2012, 6 years prior to the outbreak. A rare ESBL K. pneumoniae K2 ST628 strain harbouring a multi-drug resistant (MDR) plasmid encoding the ESBL gene blaCTX-M-15 was detected across multiple independent wards during the protracted nosocomial outbreak. Surveillance of this strain is recommended to prevent future nosocomial outbreaks.
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Affiliation(s)
- Stephen Mark Edward Fordham
- Department of Life & Environmental Sciences, Talbot Campus Fern Barrow, Bournemouth University, Poole BH12 5BB, UK; (S.M.E.F.); (M.B.); (A.M.)
| | - Francis Drobniewski
- Department of Infectious Diseases, Hammersmith Campus, Imperial College London, 8th Floor, Office 8.N10, DuCane Road, London W12 ONN, UK
- Department of Medical Microbiology, Poole Hospital, University Hospitals Dorset NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, UK (P.B.)
| | - Magdalena Barrow
- Department of Life & Environmental Sciences, Talbot Campus Fern Barrow, Bournemouth University, Poole BH12 5BB, UK; (S.M.E.F.); (M.B.); (A.M.)
| | - Melissa Hutchings
- Department of Medical Microbiology, Poole Hospital, University Hospitals Dorset NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, UK (P.B.)
| | - Kate Crowther
- Department of Medical Microbiology, Poole Hospital, University Hospitals Dorset NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, UK (P.B.)
| | - Denise Richards
- Department of Medical Microbiology, Poole Hospital, University Hospitals Dorset NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, UK (P.B.)
| | - Paul Bolton
- Department of Medical Microbiology, Poole Hospital, University Hospitals Dorset NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, UK (P.B.)
| | - Anna Mantzouratou
- Department of Life & Environmental Sciences, Talbot Campus Fern Barrow, Bournemouth University, Poole BH12 5BB, UK; (S.M.E.F.); (M.B.); (A.M.)
| | - Elizabeth Sheridan
- Department of Medical Microbiology, Poole Hospital, University Hospitals Dorset NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, UK (P.B.)
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Anderson JR, Lam NB, Jackson JL, Dorenkott SM, Ticer T, Maldosevic E, Velez A, Camden MR, Ellis TN. Progressive Sub-MIC Exposure of Klebsiella pneumoniae 43816 to Cephalothin Induces the Evolution of Beta-Lactam Resistance without Acquisition of Beta-Lactamase Genes. Antibiotics (Basel) 2023; 12:antibiotics12050887. [PMID: 37237790 DOI: 10.3390/antibiotics12050887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Bacterial exposure to antibiotic concentrations below the minimum inhibitory concentration (MIC) may result in a selection window allowing for the rapid evolution of resistance. These sub-MIC concentrations are commonly found in soils and water supplies in the greater environment. This study aimed to evaluate the adaptive genetic changes in Klebsiella pneumoniae 43816 after prolonged but increasing sub-MIC levels of the common antibiotic cephalothin over a fourteen-day period. Over the course of the experiment, antibiotic concentrations increased from 0.5 μg/mL to 7.5 μg/mL. At the end of this extended exposure, the final adapted bacterial culture exhibited clinical resistance to both cephalothin and tetracycline, altered cellular and colony morphology, and a highly mucoid phenotype. Cephalothin resistance exceeded 125 μg/mL without the acquisition of beta-lactamase genes. Whole genome sequencing identified a series of genetic changes that could be mapped over the fourteen-day exposure period to the onset of antibiotic resistance. Specifically, mutations in the rpoB subunit of RNA Polymerase, the tetR/acrR regulator, and the wcaJ sugar transferase each fix at specific timepoints in the exposure regimen where the MIC susceptibility dramatically increased. These mutations indicate that alterations in the secretion of colanic acid and attachment of colonic acid to LPS may contribute to the resistant phenotype. These data demonstrate that very low sub-MIC concentrations of antibiotics can have dramatic impacts on the bacterial evolution of resistance. Additionally, this study demonstrates that beta-lactam resistance can be achieved through sequential accumulation of specific mutations without the acquisition of a beta-lactamase gene.
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Affiliation(s)
- Jasmine R Anderson
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Nghi B Lam
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Jazmyne L Jackson
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Sean M Dorenkott
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Taylor Ticer
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Emir Maldosevic
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Amanda Velez
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Megan R Camden
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Terri N Ellis
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
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Recurrent emergence of Klebsiella pneumoniae carbapenem resistance mediated by an inhibitory ompK36 mRNA secondary structure. Proc Natl Acad Sci U S A 2022; 119:e2203593119. [PMID: 36095213 PMCID: PMC9499542 DOI: 10.1073/pnas.2203593119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Outer membrane porins in Gram-negative bacteria facilitate antibiotic influx. In Klebsiella pneumoniae, modifications in the porin OmpK36 are implicated in increasing resistance to carbapenems. An analysis of large K. pneumoniae genome collections, encompassing major healthcare-associated clones, revealed the recurrent emergence of a synonymous cytosine-to-thymine transition at position 25 (25c > t) in ompK36. We show that the 25c > t transition increases carbapenem resistance through depletion of OmpK36 from the outer membrane. The mutation attenuates K. pneumoniae in a murine pneumonia model, which accounts for its limited clonal expansion observed by phylogenetic analysis. However, in the context of carbapenem treatment, the 25c > t transition tips the balance toward treatment failure, thus accounting for its recurrent emergence. Mechanistically, the 25c > t transition mediates an intramolecular messenger RNA (mRNA) interaction between a uracil encoded by 25t and the first adenine within the Shine-Dalgarno sequence. This specific interaction leads to the formation of an RNA stem structure, which obscures the ribosomal binding site thus disrupting translation. While mutations reducing OmpK36 expression via transcriptional silencing are known, we uniquely demonstrate the repeated selection of a synonymous ompK36 mutation mediating translational suppression in response to antibiotic pressure.
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Yuan PB, Ling JH, Zhu JH, Peng C, Chen EZ, Zhong YX, Liu WT, Wang LJ, Yang L, Chen DQ. Proteomics profiling of ertapenem challenged major porin deficient carbapenem-resistant Klebsiella pneumoniae. J Proteomics 2022; 268:104715. [PMID: 36058541 DOI: 10.1016/j.jprot.2022.104715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 06/14/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent threat to human health. Major outer membrane proteins (OMPs) porin mutation is one important resistance mechanism of CRKP, and may also affect the inhibition activity of β-lactam and β-lactamase inhibitor combinations. The ertapenem-resistant K. pneumoniae strain 2018B120 with major porin mutations was isolated from a clinical patient. Genomic and time-series proteomic analyses were conducted to retrieve the ertapenem-challenged response of 2018B120. The abundance changing of proteins from PTS systems, ABC transporters, the autoinducer 2 (AI-2) quorum sensing system, and antioxidant systems can be observed. Overexpression of alternative porins was also noticed to balance major porins' defection. These findings added a detailed regulation network in bacterial resistance mechanisms and gave new insights into bypass adaptation mechanisms the porin deficient bacteria adopted under carbapenem antibiotics pressure. SIGNIFICANCE: Outer membrane porins deficiency is an important mechanism of carbapenem resistance in K. pneumoniae. Comprehensive genomic and proteomic profiling of an ertapenem-resistant K. pneumoniae strain 2018B120 gives a detailed systematic regulation network in bacterial resistance mechanisms. Overexpression of alternative porins to balance major porins' defection was noticed, giving new insights into bypass adaptation mechanisms of porin deficient bacteria.
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Affiliation(s)
- Pei-Bo Yuan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Hui Ling
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Hui Zhu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Peng
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - En-Zhong Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Xia Zhong
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wan-Ting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lin-Jing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ding-Qiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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10
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Hayashi T. [Genome analysis-based studies on bacterial genetic diversity]. Nihon Saikingaku Zasshi 2022; 77:145-160. [PMID: 36418109 DOI: 10.3412/jsb.77.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
There are a huge number of bacterial species on earth, and a huge intra-species genomic diversity are also observed in many bacteria. The high ability of bacteria to acquire foreign DNA and the presence of various mobile genetic elements contribute the generation of such genomic diversity. During the biochemical and genetic analysis of a Pseudomonas aeruginosa toxin, called cytotoxin, and its converting phage, which I first engaged in my research carrier, I became very interested in the genetic diversity of bacteria and mobile genetic elements such as bacteriophages, and realized the usefulness and power of genome analysis. Since then, I have been involved in genome analyses of various pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC), commensal bacteria of human and other animals, and bacteria or bacterial communities in natural environments. I was so lucky that I jumped in this research field at the very begging of genome analyses and experienced a very exciting time of surprisingly rapid advance in genome sequencing technologies which revolutionized a wide range of biology. In this article, I first review the main findings which our group obtained from the genome analyses on the P. aeruginosa cytotoxin converting phage and those on the evolution and genomic diversity of EHEC and related bacteria. The results of our analyses of Rickettsiaceae family genomes, which show surprisingly very low genomic diversity, and genome sequence-based analyses of an intrahospital bacterial outbreak and within-host genomic diversity are also summarized.
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Affiliation(s)
- Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
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